General Engineering

The apple orchards in Niğde, Turkiye were surveyed for ‘Candidatus Phytoplasma mali’ associated with apple proliferation disease, and the suspicious samples were tested by PCR-RFLP methods. A comprehensive study was conducted which included sampling from a total of 19 orchards from four different districts. The samples were collected according to the major symptoms of phytoplasma disease which were foliar reddening, witches’ brooms, leaf rosettes, yellowing, longer peduncles and development of undersized fruits. It was determined that six out of 62 plant samples were infected with pyhtoplasma. Also, two out of six infected samples were determined as infected by ‘Ca. P. mali’ and unexpectedly four out of six infected samples were determined as infected by ‘Ca. P. prunorum’ associated with European Stone Fruit Yellows disease. Even if the incidence of the disease (9.7%) was low, the characterized phytoplasmas were considered as a significant potential threat for these locations.
 Key words: PCR-RFLP Survey, Niğde, Apple proliferation, European stone fruit yellows

Abstract Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus ‘UBA10452’, an uncultured lineage of putative AOA in the order Nitrososphaerales (‘terrestrial group I.1b’), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.

Malakand Division in northwest Pakistan is known for delicious sweet orange, locally called Malta (Citrus sinensis). However, both quality and quantity of the citrus produce has seen a decline over the past few decades. Among production constraints, Huanglongbing (HLB) caused by phloem-limited alpha proteobacterium Candidatus Liberibacter asiaticus (CLas) -an endosymbiont of Asian Citrus Psyllid (Diaphorina citri), is of great economic significance. Therefore, we assessed HLB incidence through symptom-based surveys in major citrus growing areas of Khyber Pakhtunkhwa (KP), Northwest Pakistan. The presence or absence of CLas in the collected citrus samples was confirmed by PCR (Polymerase Chain Reaction) using three set of primers (LSS/LAS606, OI1/OI2C “16S rDNA” and MH353/MH354 “operon “nusG-rplK”). An average disease incidence of 92% and severity of 34% were recorded from main production zones in district Swat, KP. Likewise, in district Lower Dir, HLB had disease incidence and severity of 64% and 24%, respectively. Molecular diagnostics using 16S rDNA-specific primer LSS/LAS606 and OI1/OI2C, yielded characteristic bands of 500 bp and 1160 bp, from all five pooled samples from Swat district, while only two samples of Dir tested positive for both primers. Using an alternative primer MH353/MH354 (nusG-rplK) showed positive amplification for four samples from Swat and two samples of Dir with an amplicon of 631 bp. To assess the molecular diversity of the CLas, Sanger sequencing was carried out based on16S rDNA gene. Sequence analysis of 16S rDNA gene from all samples revealed maximum similarity with C. Liberibacter asiaticus. Among studied isolates, SwKjuPk-5 (MH374503) and SwMtaPk-2 (MH374500) isolates appeared to be more divergent and grouped in separate clad as compared to remaining isolates of Swat and Dir.